TB-Profiler result

Run: ERR4827811
Summary

Run ID: ERR4827811

Sample name:

Date: 2024-04-14T14:28:56.265939

Number of reads: 5415527

Percentage reads mapped: 98.21

Median coverage: 169.0

Strain: lineage4.3.3;lineage4.8

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.3 Euro-American (LAM) None 0.29
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.73
lineage4.3.3 Euro-American (LAM) RD115 0.29
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide pncA p.Leu27Pro Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
pncA 2289162 p.Leu27Pro missense_variant 0.28 pyrazinamide Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.27 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8040 p.Gly247Ser missense_variant 0.34 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.31 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 576108 p.Ala254Gly missense_variant 0.28 ethionamide
isoniazid
Rv0565c 656265 c.1204_1205delAC frameshift_variant 0.62 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 0.59 rifampicin Not assoc w R
rpoC 764995 c.1626C>G synonymous_variant 0.33 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.73 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834836 p.Met432Thr missense_variant 0.24 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.3 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2063416 p.Ala438Val missense_variant 0.68 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
katG 2156196 c.-85C>T upstream_gene_variant 0.33 isoniazid Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 0.71 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518919 p.Gly269Ser missense_variant 0.33 isoniazid
folC 2746340 p.Ala420Val missense_variant 0.29 para-aminosalicylic_acid
Rv2680 2995848 c.-257G>A upstream_gene_variant 0.67 capreomycin
thyA 3073868 p.Thr202Ala missense_variant 0.32 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.3 cycloserine
ald 3086987 p.Gln56His missense_variant 0.34 cycloserine
Rv3236c 3613636 c.-520A>G upstream_gene_variant 0.72 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 0.27 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038287 c.2418C>T synonymous_variant 0.29 pyrazinamide Not assoc w R
clpC1 4038968 c.1737G>A synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
clpC1 4039729 p.Asp326Asn missense_variant 0.69 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.29 capreomycin
amikacin
kanamycin
gid 4408156 p.Leu16Arg missense_variant 0.28 streptomycin Not assoc w R